One of the ways you can assign payments to expense accounts in Reconciler is by manually selecting an individual payment and defining what it's account should be.
Step 1 - Go to "Reconcile" view
Step 2 - Find the specific payment on the right portion of the screen that you want to assign (Use any necessary filters)
Step 3 - Click the "Account" button for that payment
Step 4 - Use the drop down to select the account you would like to assign the payment to and then click "Assign"